Sample Resequencing Stats
Note: The mutation counts shown below represent unfiltered mutation sets.
| ALE, Flask, Isolate |
Predicted Mutations |
Mean Coverage |
Total Reads |
Percent Mapped |
Mapped Reads |
Average Read Length |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,226,694 |
A→G |
43.4% |
C64C (TGT→TGC) |
pphA ← |
serine/threonine‑specific protein phosphatase 1 |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,226,694 | 0 | A | G | 43.4%
| 16.5
/ 59.0
| 76 | C64C (TGT→TGC) | pphA | serine/threonine‑specific protein phosphatase 1 |
| Reads supporting (aligned to +/- strand): ref base A (14/29); new base G (23/10); total (37/39) |
| Fisher's exact test for biased strand distribution p-value = 2.38e-03 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CATCGCCATCTGTTCATGATTGCCTCTTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGTA > minE/1226631‑1226746
|
catcGCCATCTGTTCATGATTGCCTCTTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAAc > 1:309554/1‑68 (MQ=255)
catcGCCATCTGTTCATGATTGCCTCTTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAAc > 1:3177134/1‑68 (MQ=255)
tGTACATGATTGCCTCTTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGc > 1:1663629/1‑69 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:2298021/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:2670721/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:2914338/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:1576138/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:3371053/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:387002/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:682771/69‑1 (MQ=255)
tctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:1219860/69‑1 (MQ=255)
tctTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCAcgatcgat < 1:1580950/69‑1 (MQ=255)
tctTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCAcgatcgat < 1:1841501/69‑1 (MQ=255)
ctTACCGCACGAACCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:190388/68‑1 (MQ=255)
tgCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2659134/67‑1 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACTTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2441347/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCAcgatc > 1:2637488/3‑56 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGtct > 1:705634/3‑66 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1073038/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:3381897/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:248781/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2601026/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:76517/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2709938/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2915468/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:3150908/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:653587/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:3288108/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:3353033/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:353411/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1317218/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1322765/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1332924/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1795506/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:1810392/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2050976/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTccc > 1:2017563/3‑69 (MQ=255)
cgaaCCCAATGTTGTTCCAGTAACTGCAGGCAACGTAAACTTTGCGGCCCACGATCGATAACGTCTcc > 1:2014330/3‑68 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt > 1:98617/1‑64 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:3134600/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt > 1:2929783/1‑64 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:186757/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:1945371/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2012667/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2390109/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2135836/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2266644/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:2074713/64‑1 (MQ=255)
caAACCCAATGTTGTTCCAGTAACCGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt > 1:2685687/1‑64 (MQ=255)
aaaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt > 1:1047271/1‑63 (MQ=255)
aaaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:1636008/63‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:273470/62‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCa < 1:203110/68‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCa < 1:3080089/68‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCa < 1:230531/68‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCa < 1:3426240/68‑1 (MQ=255)
aaCCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCa < 1:3345703/68‑1 (MQ=255)
ttgttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATaa > 1:3329009/1‑68 (MQ=255)
ttgttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATaa > 1:328777/1‑68 (MQ=255)
ttgttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATaa > 1:3241094/1‑68 (MQ=255)
ttgttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATaa > 1:3067990/1‑68 (MQ=255)
tgttCCAGTAACT‑CAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGTa > 1:1394643/1‑69 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:1635459/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:2106591/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:2066612/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:23565/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:2189760/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:1389335/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:384259/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt > 1:143071/1‑68 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:1452873/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:1548902/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGt < 1:2614009/68‑1 (MQ=255)
gttCCAGTAACTGCAGACAACGTAAACTTTGCGGCCAAcgatcg > 1:1770731/1‑44 (MQ=255)
aGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGt < 1:3345175/46‑1 (MQ=255)
aaCTGCAGGCAACGTAAACTTTGCGGCCCAcgatcgat < 1:3376218/38‑1 (MQ=255)
|
CATCGCCATCTGTTCATGATTGCCTCTTACCGCACAAACCCAATGTTGTTCCAGTAACTGCAGACAACGTAAACTTTGCGGCCCACGATCGATAACGTCTCCCACTGAGATAAGTA > minE/1226631‑1226746
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
